Abstract
Routine surveillance and surveillance in response to influenza outbreaks in avian species in Vietnam in 2009–2013 resulted in the isolation of numerous H5N1 influenza viruses of clades 1.1.2, 2.3.2.1a, 2.3.2.1b, 2.3.2.1c, and 2.3.4.1. Consistent with other studies, we found that viruses of clade 2.3.2.1c were dominant in Vietnam in 2013 and circulated in the northern, central, and southern parts of the country. Phylogenetic analysis revealed reassortment among viruses of clades 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c; in contrast, no reassortment was detected between clade 2.3.2.1 viruses and viruses of clades 1.1.2 or 2.3.4.1, respectively. Deep-sequencing of 42 of the 53 isolated H5N1 viruses revealed viral subpopulations encoding variants that may affect virulence, host range, or sensitivity to antiviral compounds; virus isolates containing these subpopulations may have a higher potential to transmit and adapt to mammals. Among the viruses sequenced, a relatively high number of non-synonymous nucleotide polymorphisms was detected in a virus isolated from a barn swallow, possibly suggesting influenza virus adaption to this host.
Highlights
Pathogenic avian influenza (HPAI) viruses of the H5N1 subtype were first identified in Vietnam in 2001 (Nguyen et al, 2005)
Since their first emergence in 1997 in Hong Kong, Highly pathogenic avian influenza (HPAI) H5N1 viruses have evolved into multiple clades and subclades that are defined on the basis of the sequence of the viral surface glycoprotein hemagglutinin (HA), the major viral antigen
We carried out surveillance in live bird markets in different provinces of Vietnam (Figure 2) by collecting oropharyngeal swabs and cloacal samples from apparently healthy chickens and ducks (Table 1)
Summary
Pathogenic avian influenza (HPAI) viruses of the H5N1 subtype were first identified in Vietnam in 2001 (Nguyen et al, 2005). H5N1 infections have been reported in Vietnam, but HPAI H5N1 viruses remain a threat to the country’s public health Since their first emergence in 1997 in Hong Kong, HPAI H5N1 viruses have evolved into multiple clades and subclades that are defined on the basis of the sequence of the viral surface glycoprotein hemagglutinin (HA), the major viral antigen. Reassortment resulted in the emergence of clade 2.3.4.4 H5N6 viruses in Vietnam and other Southeast Asian countries (Wong et al, 2015; Chu et al, 2016; Lee et al, 2017; Nguyen et al, 2017). Characterization of the HPAI H5N1 samples by phylogenetic analysis, Sanger sequencing, and deep-sequencing of 42 of the samples revealed multiple genotypes and potentially mammalian-adapting amino acid changes in some of the viral subpopulations
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